You have to fully isolate the issue. You still have the amplifier, speaker terminals, and tower wiring to consider.
Re-check the voltage at the amplifier terminals plus the ground. Probably not the cause but it must be eliminated.
Run a temporary jumper wire from the amplifier output in question to the speaker thereby circumventing the tower harness. No input RCA. Try the same with a different speaker.
If the noise is really horrific, place a 100 mfd non-polarized capacitor in series with the test speaker to offer some protection while going through your tests.
From your description thus far, I suspect that you have an internal amplifier failure.